Plant diseases can be a frustrating addition to any growing scenario. However, they come with the territory, they're the "nature of the beast" so to say. The fact is, many plant diseases are always there, but only come out to play when the conditions are right, or wrong. High humidity allows molds to take hold; lack of oxygen in the root zone allows pathogens including fusarium, pythium, rhizoctonia, phytopthera, sclerotinia, etc. to develop all with varying degrees of virulence. The best defense against plant diseases is a healthy plant and a healthy plant environment. However, maybe you have troubleshot every possible scenario for deficiency, dereliction, or pest infestation and you are still experiencing a problem. Odds are your plant is sick.
Diseases can attack the foliage growth or the root growth. Here we will discuss identifying, troubleshooting, and eradicating diseases from both scenarios.

Foliage Disease
Foliage diseases take many different forms and are not categorized very well. They manifest themselves as mildews (Powdery mildew, Downey mildew), blights

Blight : Affecting a long list of different plant species, each in a slightly different manner, blight is a bacterial disease. The disease spreads rapidly in wet conditions, generally turning whole or parts of leaves brown and black. Highly contagious: if you suspect your plants are suffering from blight, trim off dead or dying plant material at least two inches below infected material, sterilizing your pruners between each cut.
(Early and Late blight, Bacterial Leaf blight), molds (Gray mold, Black mold), rusts, and myriad other forms. Many times it is hard to specifically identify a disease form visual inspection because a plant can only reciprocate a stress in so many ways. However, there are many that can be noticed right away, such as Black Spot or Powdery Mildew that are common on roses and many other plants. Use the disease finder here to help identify your specific infection, but the good news is that there are natural products that eliminate and control almost any plant pathogen. Don't go the chemical fungicide rout you're only sending the problem somewhere else.

Damping-off fungi

Damping-off fungus : Disease that attacks young seedlings and cuttings causing stem to rot at base. Over watering and cool wet soils favor development of the disease. The damping-off fungi may attack the seed prior to germination, or they may attack after the seed has germinated but before the seedling has emerged above the soil line. Infected seed becomes soft and mushy turning a brown to black color, and it eventually disintegrates. Seeds that have germinated and become infected develop water-soaked spots that enlarge and turn brown. The infected tissue collapses, resulting in death of the seedling. Penetration and death of seeds before they emerge is termed preemergence damping-off.
is an affliction that attacks at or below the media line, but is most common in seeds and starts. Damping-off can be controlled and eliminated after infection, but is most easily treated via a preventative seed soak. For further info refer here.

Root Disease

Odds are every hydroponic gardener, especially a beginner, has experienced a root disease. The good news is that in hydro you can see the roots and can directly diagnose the issue. Root diseases are not as common in soil or outdoors due to soils buffering capacity and the presence of microorganisms and materials capable of creating a balance in an ecosystem. The reality is that pathogens, such as pythium, fusarium, etc. are always prevalent in reservoirs; it is simply waiting for the right conditions to come out and play. The best way to ensure you will never have a root disease issue is by using a preventative treatment utilizing beneficial organisms. Root diseases are normally not recognized until there is some repercussion of stress in the foliage of the plant. Upon inspection of the roots they are brown or black and slimy. Depending on how far the disease has progressed and how valuable your plants are to you it is often best to start your crop over being mindful of what you were doing and troubleshooting potential causes so as not to replicate the disease issue and conditions. However, it is possible to correct an infection if it is not so far gone in the first place. Root pruning is prudent, especially if the disease has not progressed to the entire root system. For a more in depth discussion of root logistics refer to the "root" sections on this website.